knitr::opts_chunk$set(
    echo = TRUE,
    message = FALSE,
    warning = FALSE
)

library(tidyverse) #used for data wrangling and viz
library(here) #simplifies file paths
library(rsample) #used to split data
library(janitor) #used to clean data names
library(corrplot) #for correlation viz
library(VIM) #for missing data viz
library(mice) #for imputing missing data
library(ggfortify) #for PCA viz
library(fastDummies) #for dummy coding
library(caret) #for cross validation
library(class) #for knn
library(gbm) #for boosted trees modeling
library(randomForest) #for random forest modeling
library(maptools)
library(RColorBrewer)
library(classInt)
library(ggplot2)
library(ggrepel)
library(mapproj)
library(viridis)
library(pander)
library(knitr)
#turns scientific notation off
options(scipen = 100)

#some of our workflow includes randomness. here we set a seed so our workflow can be reproduced without worrying about random variation
set.seed(123)

1 Introduction

The purpose of this project is to use machine learning techniques to predict which wildfires will grow to a catastrophic size. Our most accurate model will then be used to assess how global climate change may influence a wildfires predicted size.

1.1 Background

fire situation in North America, climate change, etc

1.2 Why this model is useful

What will it be used for?

1.3 Data and Packages Used

This dataset is available on Kaggle. It is a subset of larger fires

Important attributes include

  • fire_size - the size of the fire in acres

  • stat_cause_descr - the cause of the fire

  • vegetation - code corresponding to vegetation type

  • temp_cont - temperature (Celsius) when the fire was contained

A complete codebook is available in the project file

#read in dataset
us_wildfire <- read_csv(here("archive", "FW_Veg_Rem_Combined.csv"))
#Following to the National Geographic Education
us_wildfire$region = "NorthEast"
us_wildfire[which(us_wildfire$state %in% c("AK", "WA", "OR", "CA", "NV", "ID", "MT", "WY", "UT", "CO")),"region"] = "West"
us_wildfire[which(us_wildfire$state %in% c("AZ", "NM", "TX", "OK")), "region"] = "SouthWest"
us_wildfire[which(us_wildfire$state %in% c("ND", "SD", "NE", "KS", "MN", "IA", "MO", "WI", "IL", "MI", "IN", "OH")), "region"] = "MidWest"
us_wildfire[which(us_wildfire$state %in% c("AR", "LA", "MS", "AL", "GA", "FL", "SC", "NC", "TN", "KY", "VA", "WV")), "region"] = "SouthEast"

us_wildfire$year_diff = us_wildfire$disc_pre_year - min(us_wildfire$disc_pre_year)

2 Methods

Our methods involved cleaning the data, conducting exploratory analysis, imputing missing data, and using Principle Components Analysis to reduce the number of features.

2.1 Cleaning Data

To clean the data we first converted all column names to lower snake case using the clean_names() function. Then we selected only the columns were were interested in using, thereby removing all the meaningless columns.

us_wildfire_clean <- us_wildfire %>% 
  dplyr::select(fire_name:year_diff) %>% #select columns we want to use
  clean_names() #convert to lowercase snake

We are interested in using weather to predict fire size, so we filter out observations where the weather data was not associated with the fire observation.

There are some weather observations for which every weather field is 0. This seems unlikely, especially for temperature and humidity observations. So we will replace them with NAs. Since precipitation is frequently 0, we will not replace all 0 with NAs in the precipitation column.

Instead, we will follow the pattern of NAs seen in other the other weather columns. We can see that there is a clear pattern in the missing weather data. when temp_pre_30 is missing, so is wind_pre_30 and humidity_pre_30. We will assume this extends to prec_pre_30 and replace that 0 with a NA.

#filter out observations that do not have a weather file
us_wildfire_clean <- us_wildfire_clean %>% 
  filter(weather_file != "File Not Found")

#replace 0 with NA
us_wildfire_clean <- us_wildfire_clean %>%
  mutate_at(vars(temp_pre_30:hum_cont), ~na_if(., 0.0000000))

#when temp, wind, and humidity are missing, we suspect precipitation is as well.
#we use a case when statement to replace these zeros with NAs
us_wildfire_clean <- us_wildfire_clean %>% 
  mutate(prec_pre_30 = case_when(is.na(temp_pre_30) & is.na(hum_pre_30) & is.na(wind_pre_30) ~ NA_real_,
                                      TRUE ~ prec_pre_30)) %>% 
  mutate(prec_pre_15 = case_when(is.na(temp_pre_15) & is.na(hum_pre_15) & is.na(wind_pre_15) ~ NA_real_,
                                      TRUE ~ prec_pre_15)) %>% 
  mutate(prec_pre_7 = case_when(is.na(temp_pre_7) & is.na(hum_pre_7) & is.na(wind_pre_7) ~ NA_real_,
                                      TRUE ~ prec_pre_7)) %>% 
  mutate(prec_cont = case_when(is.na(temp_cont) & is.na(hum_cont) & is.na(wind_cont) ~ NA_real_,
                                      TRUE ~ prec_cont))

Information about vegetation was stored in a numeric form, where each number represented a class of vegetation. The key for the vegetation codes was in the provided metadata. For ease of interpretation, we replaced the numeric code with a short description the vegetation type.

According the metadata for this data set, the vegetation was created by interpolating most likely vegetation based on latitude and longitude. The most common vegetation type is listed as “Polar Desert/Rock/Ice” and this seems very unlikely. Although we keep the vegetation feature in the data, we have doubts about its accuracy.

#Here we label vegetation according to the provided codebook
us_wildfire_clean <- us_wildfire_clean %>% 
  mutate(vegetation_classed = case_when(
    vegetation == 12 ~ "Open Shrubland",
    vegetation == 15 ~ "Polar Desert/Rock/Ice",
    vegetation == 16 ~ "Secondary Tropical Evergreen Broadleaf Forest",
    vegetation == 4 ~ "Temperate Evergreen Needleleaf Forest TmpENF",
    vegetation == 9 ~ "C3 Grassland/Steppe",
    vegetation == 14 ~ "Desert"
  ))

Our final data cleaning action was to clean up date columns. Since there are redundant date columns, we chose to keep only month and year as variables. We also reclassified months into seasons, so there would be fewer factor levels or dummy coding involved when it came time to prepare the data for modeling.

#keep month and year as variables
us_wildfire_clean <- us_wildfire_clean %>% 
  dplyr::select(-disc_clean_date, 
         -disc_date_pre, 
         -cont_clean_date, 
         -disc_pre_month,
         -disc_date_final,
         -cont_date_final,
         -putout_time)

#we also reclassify months into seasons, to reduce factor levels
us_wildfire_clean <- us_wildfire_clean %>% 
  mutate(season = case_when(discovery_month %in% c("Apr", "May", "Jun") ~ "Spring",
                            discovery_month %in% c("Jul", "Aug", "Sep") ~ "Summer",
                            discovery_month %in% c("Oct", "Nov", "Dec") ~ "Fall",
                            discovery_month %in% c("Jan", "Feb", "Mar") ~ "Winter")) %>% 
  select(-discovery_month)

2.2 Exploratory Analysis

Our next step was to explore the data. We created several figures to investigate fire observations, as well as the pattern of missing data and the correlation between variables.

First we investigated fire size through time. This figure shows that the total acrage burned per year has been increasing almost linearly since 1990. This is a clue that Year might be a useful feature in our models.

#summarise acres per year burned
acres_per_year <- us_wildfire_clean %>% 
  group_by(disc_pre_year) %>% 
  summarise(acres_burned = sum(fire_size))

#fire size (finalized graph)
ggplot(data = acres_per_year) + 
  geom_point(aes(x = disc_pre_year, 
                 y = acres_burned, 
                 size = acres_burned, 
                 color = acres_burned)) +
  scale_color_continuous(high = "firebrick", low = "goldenrod1") +
  labs(x = "Year", y = "Total Acres Burned", 
       title = "Total acres burned per year from 1990 to 2015") +
  theme_minimal() +
  theme(legend.position = "none")

We also looked at the most common causes of fires. We found that most fires were started by debris burning, followed by arson. Yikes! We were also surprised that a children were frequently listed as the cause of wildfires.

#most common causes of fire
fire_causes <- us_wildfire_clean %>% 
  group_by(stat_cause_descr) %>% 
  count()

#cause (finalized)
ggplot(data = fire_causes, aes(y = reorder(stat_cause_descr, n), x = n)) +
  geom_col(aes(fill = n)) +
  scale_fill_gradient(high = "firebrick", low = "goldenrod1") +
  labs(x = "Number of Fires", 
       y = "Cause",
       tite = "Number of fires per listed starting cause") +
  theme_minimal() +
  theme(legend.position = "none")

2.2.1 Map of regions

us_wildfire_clean$class_fac = factor(us_wildfire_clean$fire_size_class, levels = c("A", "B", "C", "D", "E", "F", "G"))

us <- map_data("world", 'usa')

state <- map_data("state")

state$region2 = "NorthEast"
state[which(state$region %in% c("alaska", "washington", "oregon", "california", "nevada", "idaho", "montana", "utah", "wyoming", "colorado")), "region2"] = "West"
state[which(state$region %in% c("arizona", "new mexico", "oklahoma", "texas")), "region2"] = "SouthWest"
state[which(state$region %in% c("north dakota", "south dakota", "nebraska", "kansas", "minnesota", "iowa", "missouri", "wisconsin", "illinois", "indiana", "michigan", "ohio")), "region2"] = "MidWest"
state[which(state$region %in% c("arkansas", "louisiana", "mississippi", "alabama", "florida", "georgia", "south carolina", "north carolina", "tennessee", "kentucky", "virginia", "west virginia")), "region2"] = "SouthEast"

#state$region = as.factor(state$region)

ggplot(data=state, aes(x=long, y=lat, group = region)) + 
  geom_polygon(aes(fill=region2)) +
  ggtitle("US Region")+
  guides(fill=guide_legend(title="Region"))+
  coord_map(projection = "sinusoidal", xlim=c(-120, -75), ylim = c(25, 50))

2.2.2 Map of fires

2.2.2.1 The spatial distribution of wildifres

ggplot() + 
  geom_polygon(data=state, aes(x=long, y=lat, group=group), color = "white", fill = "grey") + 
  geom_point(data = us_wildfire_clean, aes(x=longitude, y = latitude, color = class_fac)) +
  scale_color_brewer(palette = "YlOrRd")+
  ggtitle("US Wildfire Distribution")+
  guides(color=guide_legend(title="Wild Fire Scale"))+
  coord_map(projection = "sinusoidal", xlim=c(-120, -75), ylim = c(25, 50))

2.2.3 When we divide it to three periods, we can see the wildfire risk has been growing in Western parts of the US.

ggplot() + 
  geom_polygon(data=state, aes(x=long, y=lat, group=group), color = "white", fill = "grey") + 
  geom_point(data = us_wildfire_clean[which(us_wildfire_clean$wstation_byear < 1970),], aes(x=longitude, y = latitude, color = class_fac)) +
  scale_color_brewer(palette = "YlOrRd")+
  ggtitle("US Wildfire Distribution before 1970")+
  guides(color=guide_legend(title="Wild Fire Scale"))+
  coord_map(projection = "sinusoidal", xlim=c(-120, -75), ylim = c(25, 50))

ggplot() + 
  geom_polygon(data=state, aes(x=long, y=lat, group=group), color = "white", fill = "grey") + 
  geom_point(data = us_wildfire_clean[which(us_wildfire_clean$wstation_byear >= 1970 & us_wildfire_clean$wstation_byear < 2000),], aes(x=longitude, y = latitude, color = class_fac)) +
  scale_color_brewer(palette = "YlOrRd")+
  ggtitle("US Wildfire Distribution 1970-2000")+
  guides(color=guide_legend(title="Wild Fire Scale"))+
  coord_map(projection = "sinusoidal", xlim=c(-120, -75), ylim = c(25, 50))

ggplot() + 
  geom_polygon(data=state, aes(x=long, y=lat, group=group), color = "white", fill = "grey") + 
  geom_point(data = us_wildfire_clean[which(us_wildfire_clean$wstation_byear >= 200),], aes(x=longitude, y = latitude, color = class_fac)) +
  scale_color_brewer(palette = "YlOrRd")+
  ggtitle("US Wildfire Distribution after 2000")+
  guides(color=guide_legend(title="Wild Fire Scale"))+
  coord_map(projection = "sinusoidal", xlim=c(-120, -75), ylim = c(25, 50))

2.2.4 Density graph

ggplot() + 
  geom_density(data= us_wildfire_clean[which(us_wildfire_clean$wstation_byear <= 1970 & us_wildfire_clean$fire_size > 100),], aes(x = fire_size, y=..density..),
               alpha=.3,
               colour="dodgerblue", fill="dodgerblue") + 
  geom_density(data= us_wildfire_clean[which(us_wildfire_clean$wstation_byear >= 1970 & us_wildfire_clean$fire_size > 100 & us_wildfire_clean$wstation_byear < 2000),], aes(x = fire_size, y=..density..),
               alpha=.3,
               colour="yellow3", fill="yellow3") + 
  geom_density(data= us_wildfire_clean[which(us_wildfire_clean$wstation_byear >= 2000 & us_wildfire_clean$fire_size > 100),], aes(x = fire_size, y=..density..),
               alpha=.3,
                 colour="firebrick3", fill="firebrick3") + 
  xlim(10000, 100000) + 
  ggtitle("Wildfire Severeity")

2.2.5 Exploring Missing Data and Correlation

As part of our exploratory analysis, we we looked at the pattern of missing data. This figure shows missing data in red. You can see that most missing data is concentrated in the weather columns, and the name of the fire is also often missing.

#missing data plot
aggr_plot <- aggr(us_wildfire_clean, 
                  col = c('yellow','red'), 
                  numbers = TRUE, 
                  sortVars = TRUE, 
                  labels = names(us_wildfire_clean), 
                  cex.axis = .7, 
                  gap = 2, 
                  ylab = c("Histogram of missing data","Pattern"))

## 
##  Variables sorted by number of missings: 
##            Variable      Count
##           fire_name 0.50282019
##            hum_cont 0.42786638
##           wind_cont 0.41558884
##           temp_cont 0.41002139
##           prec_cont 0.41002139
##  vegetation_classed 0.17480307
##           hum_pre_7 0.14329476
##          hum_pre_15 0.12783234
##          wind_pre_7 0.12250802
##          temp_pre_7 0.11173782
##          prec_pre_7 0.11173782
##         wind_pre_15 0.10663231
##         temp_pre_15 0.09571623
##         prec_pre_15 0.09571623
##          hum_pre_30 0.09413595
##         wind_pre_30 0.07308179
##         temp_pre_30 0.06216571
##         prec_pre_30 0.06216571
##           fire_size 0.00000000
##     fire_size_class 0.00000000
##    stat_cause_descr 0.00000000
##            latitude 0.00000000
##           longitude 0.00000000
##               state 0.00000000
##       disc_pre_year 0.00000000
##       wstation_usaf 0.00000000
##          dstation_m 0.00000000
##       wstation_wban 0.00000000
##      wstation_byear 0.00000000
##      wstation_eyear 0.00000000
##          vegetation 0.00000000
##            fire_mag 0.00000000
##        weather_file 0.00000000
##          remoteness 0.00000000
##              region 0.00000000
##           year_diff 0.00000000
##              season 0.00000000
##           class_fac 0.00000000

We hypothesized that weather variables were correlated. To test this out, we created a correlation matrix.

This figure shows that there is a strong correlation with each set of variables. I.e. the 7 day average temperature is correlated with the 30 day average temperature. This is not surprising!

#create a dataframe of weather
weather <- us_wildfire_clean %>% 
  dplyr::select(temp_pre_30:prec_cont)

#create a correlation matrix (omitting NAs)
cor_matrix <- cor(weather, use = "complete.obs")

#create a visualization
corrplot(cor_matrix, type = "upper", order = "hclust", 
         tl.col = "black", tl.srt = 45)

2.3 Model Preparation

After exploring our data, we were ready to prepare it for modeling. We first split the data into test and training data, then do some data manipulations separately on the test and training data.

2.3.1 Splitting Data

Before we split the data, we got rid of even more variables. Some we used in exploratory data analysis but decided not to use in modeling, and some were just not useful. Then we split our data into 80% training and 20% testing data. Because fire size is heavily skewed towards smaller fires, we used stratified sampling.

There are 32903 observations in the training set and 8229 observations in the test set.

#first we make a data frame containing only variables we want to use in our models
fire_modeling_df <- us_wildfire_clean %>%
  dplyr::select(-fire_name, #remove fire name
         -fire_size_class, #remove fire size class
         -class_fac, #which is also a size class
         -state, #because we have regions
         -disc_pre_year, #because we have year_diff to represent year
         -wstation_usaf, #remove weather station name
         -wstation_wban, #remove this (not described in codebook)
         -wstation_byear, #remove station year installed
         -wstation_eyear, #remove station year ended data recording
         -weather_file, #remove name of weather file
         -dstation_m, #remove distance of weather station to fire
         -vegetation #remove vegetation because we already have it classed
         )

#define split parameters
us_wildfire_split <- fire_modeling_df %>% 
  initial_split(prop = 0.8, strata = "fire_size")

#write split data to data frames
fire_train <- training(us_wildfire_split)
fire_test <- testing(us_wildfire_split)

#set up folds in training data for cross validation
train_folds <- vfold_cv(fire_train, v = 10, repeats = 5)

2.3.2 Imputing Missing Data

Next we impute (or replace) all the missing data in our weather columns. We use the predictive mean method of imputation, which works by predicting the value of the missing variable using regression, then randomly choosing a similar value from a pool of candidates that are found in the data. We use the default values of m = 5 and maxit = 5 to reduce computing time, but increasing the number of multiple imputations using the m argument and increasing the number of iterations through the maxit argument could increase accuracy.

#select weather cols     
weather_train <- fire_train %>%
  select(temp_pre_30:prec_cont)

weather_test <- fire_test %>%
  select(temp_pre_30:prec_cont)

#select cols not in weather
notweather_train <- fire_train %>%
  select(-colnames(weather_train))

notweather_test <- fire_test %>%
  select(-colnames(weather_test))

#imputation of weather data
weather_train_imputed <- mice(weather_train, m=5, maxit=5, meth='pmm', seed=500) %>% 
  complete()


weather_test_imputed <- mice(weather_test, m=5, maxit=5, meth='pmm', seed=500) %>% 
  complete()

2.3.3 Principle Components

#Do PCA on both test and train data separately
weather_train_PCA <- weather_train_imputed %>%
  scale(center = T, scale = T) %>%  #first scale and center the data
  prcomp(rank. = 4) #do PCA


#weather_train_PCA$x

#Do PCA on both test and train data separately
weather_test_PCA <- weather_test_imputed %>%
  scale(center = T, scale = T) %>%  #first scale and center the data
  prcomp(rank. = 4)

#Make a PCA bi-plot
autoplot(weather_train_PCA, 
         data = weather_train,
         loadings = TRUE, 
         loadings.label = TRUE,
         loadings.label.hjust = 1.2) +
  theme_classic() +
  labs(caption = "Principle Component Analysis Bi-plot of Weather Training Data")

#put data back together

#bind imputed weather data to rest of rows
fire_train_complete <- cbind(notweather_train, weather_train_PCA$x) %>% 
  na.omit()

fire_test_complete <- cbind(notweather_test, weather_test_PCA$x) %>% 
  na.omit()

2.4 Modeling As a Regression Problem

First of all, we applied multiple linear regression models on the dataset. The performance of the multiple linear regression will present why we need to apply machine learning approaches. First of all, I started with the whole variables including principal components. And then, less relevant variables were deleted from to find the optimal multiple linear regression model.

lm_whole = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete)
summary(lm_whole) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 3429 386.1 8.88
PC1 -738.6 39.65 -18.63
PC2 -180.7 39.4 -4.587
PC3 268.1 48.03 5.582
PC4 -466.9 54.57 -8.557
year_diff 57.18 12.22 4.68
remoteness -9138 631.2 -14.48
vegetation_classedDesert -979.2 683.4 -1.433
vegetation_classedOpen Shrubland -1474 308.7 -4.775
vegetation_classedPolar Desert/Rock/Ice -616.3 307.2 -2.006
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest -1692 314.2 -5.384
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF -188.8 612.9 -0.3081
stat_cause_descrCampfire 2165 523 4.139
stat_cause_descrChildren -584.4 515.4 -1.134
stat_cause_descrDebris Burning -238 234.4 -1.015
stat_cause_descrEquipment Use 626.9 334.7 1.873
stat_cause_descrFireworks -1309 1219 -1.074
stat_cause_descrLightning 5165 297.3 17.37
stat_cause_descrMiscellaneous 334.6 271.3 1.233
stat_cause_descrMissing/Undefined 512.9 327.2 1.567
stat_cause_descrPowerline 1091 761.7 1.432
stat_cause_descrRailroad -157.8 585.1 -0.2697
stat_cause_descrSmoking -575.3 547.7 -1.05
stat_cause_descrStructure -527.5 1974 -0.2672
  Pr(>|t|)
(Intercept) 0.0000000000000000007079
PC1 0.00000000000000000000000000000000000000000000000000000000000000000000000000006054
PC2 0.000004517
PC3 0.00000002406
PC4 0.00000000000000001215
year_diff 0.000002886
remoteness 0.00000000000000000000000000000000000000000000002534
vegetation_classedDesert 0.1519
vegetation_classedOpen Shrubland 0.000001807
vegetation_classedPolar Desert/Rock/Ice 0.04483
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.00000007335
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.758
stat_cause_descrCampfire 0.00003497
stat_cause_descrChildren 0.2568
stat_cause_descrDebris Burning 0.3101
stat_cause_descrEquipment Use 0.06102
stat_cause_descrFireworks 0.2829
stat_cause_descrLightning 0.0000000000000000000000000000000000000000000000000000000000000000003096
stat_cause_descrMiscellaneous 0.2174
stat_cause_descrMissing/Undefined 0.117
stat_cause_descrPowerline 0.152
stat_cause_descrRailroad 0.7874
stat_cause_descrSmoking 0.2935
stat_cause_descrStructure 0.7894
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
27229 12420 0.05937 0.05858 
lm_whole2 <- update(lm_whole, . ~ . - stat_cause_descr)
summary(lm_whole2) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 5079 346.2 14.67
PC1 -1041 36.71 -28.37
PC2 -54.51 39.16 -1.392
PC3 198.2 48.17 4.114
PC4 -504.1 54.68 -9.22
year_diff 61.56 12.08 5.098
remoteness -8807 633 -13.91
vegetation_classedDesert -1449 688.1 -2.106
vegetation_classedOpen Shrubland -2705 303.6 -8.91
vegetation_classedPolar Desert/Rock/Ice -1128 308 -3.662
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest -3001 308.4 -9.731
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF -250 617.5 -0.4048
  Pr(>|t|)
(Intercept) 0.000000000000000000000000000000000000000000000001574
PC1 1.814e-174
PC2 0.164
PC3 0.00003896
PC4 0.00000000000000000003176
year_diff 0.0000003451
remoteness 0.00000000000000000000000000000000000000000007579
vegetation_classedDesert 0.03525
vegetation_classedOpen Shrubland 0.0000000000000000005391
vegetation_classedPolar Desert/Rock/Ice 0.000251
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.0000000000000000000002423
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.6856
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
27229 12523 0.04317 0.04279

When we compare the whole region’s regression results, it shows that the updated model is superior than the others.

lm_sw = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete[which(fire_train_complete$region == "SouthWest"),])
summary(lm_sw) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 1392 1360 1.024
PC1 -600.3 91.77 -6.542
PC2 -632.1 91.56 -6.903
PC3 175.1 214.5 0.8164
PC4 -599.4 200.7 -2.987
year_diff 106.7 32.31 3.301
remoteness -8083 3743 -2.159
vegetation_classedPolar Desert/Rock/Ice -93.29 620.6 -0.1503
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest -456.3 424.3 -1.075
stat_cause_descrCampfire 7782 1496 5.201
stat_cause_descrChildren -1297 1710 -0.7583
stat_cause_descrDebris Burning -184.5 667 -0.2766
stat_cause_descrEquipment Use -634.4 805.9 -0.7872
stat_cause_descrFireworks -1586 3343 -0.4744
stat_cause_descrLightning 2256 780 2.892
stat_cause_descrMiscellaneous 498.2 686.9 0.7254
stat_cause_descrMissing/Undefined 2786 913.5 3.049
stat_cause_descrPowerline 934.5 1229 0.7603
stat_cause_descrRailroad -827.6 2254 -0.3671
stat_cause_descrSmoking -802.6 1358 -0.5908
stat_cause_descrStructure 432.9 8078 0.0536
  Pr(>|t|)
(Intercept) 0.3059
PC1 0.00000000006565
PC2 0.000000000005581
PC3 0.4143
PC4 0.002832
year_diff 0.0009695
remoteness 0.03085
vegetation_classedPolar Desert/Rock/Ice 0.8805
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.2823
stat_cause_descrCampfire 0.0000002044
stat_cause_descrChildren 0.4483
stat_cause_descrDebris Burning 0.7821
stat_cause_descrEquipment Use 0.4312
stat_cause_descrFireworks 0.6352
stat_cause_descrLightning 0.003842
stat_cause_descrMiscellaneous 0.4682
stat_cause_descrMissing/Undefined 0.002302
stat_cause_descrPowerline 0.4471
stat_cause_descrRailroad 0.7135
stat_cause_descrSmoking 0.5547
stat_cause_descrStructure 0.9573
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
6326 13948 0.03803 0.03498 
lm_sw2 <- update(lm_sw, . ~ . - stat_cause_descr - PC2 - remoteness)
summary(lm_sw2) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) -389.4 569.6 -0.6837
PC1 -715.9 81.23 -8.813
PC3 450.8 210.5 2.141
PC4 -446.3 197.7 -2.257
year_diff 86.15 31.08 2.772
vegetation_classedPolar Desert/Rock/Ice 1261 583.3 2.163
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 176.6 410.3 0.4305
  Pr(>|t|)
(Intercept) 0.4942
PC1 0.00000000000000000156
PC3 0.03227
PC4 0.02403
year_diff 0.005586
vegetation_classedPolar Desert/Rock/Ice 0.0306
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.6669
Fitting linear model: fire_size ~ PC1 + PC3 + PC4 + year_diff + vegetation_classed
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
6326 14053 0.02124 0.02031 
lm_se = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete[which(fire_train_complete$region == "SouthEast"),])
summary(lm_se) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) -2518 2241 -1.123
PC1 -6.769 28.15 -0.2404
PC2 -74.23 20.92 -3.549
PC3 37.7 20.13 1.873
PC4 9.194 27.98 0.3286
year_diff 2.743 5.846 0.4692
remoteness 19527 468.7 41.66
vegetation_classedOpen Shrubland -987 2240 -0.4406
vegetation_classedPolar Desert/Rock/Ice -746.6 2241 -0.3331
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest -847 2240 -0.3781
stat_cause_descrCampfire 18.38 238 0.07723
stat_cause_descrChildren 640.6 218.4 2.933
stat_cause_descrDebris Burning 227.5 91.92 2.475
stat_cause_descrEquipment Use 430.6 161.2 2.672
stat_cause_descrFireworks 251.5 1041 0.2417
stat_cause_descrLightning 1371 156.4 8.768
stat_cause_descrMiscellaneous 258.2 134.8 1.915
stat_cause_descrMissing/Undefined 242.6 149.5 1.623
stat_cause_descrPowerline 297.4 918.3 0.3239
stat_cause_descrRailroad 572.4 219.7 2.605
stat_cause_descrSmoking 354.6 248.7 1.426
stat_cause_descrStructure 178 894 0.1991
  Pr(>|t|)
(Intercept) 0.2613
PC1 0.81
PC2 0.0003882
PC3 0.06109
PC4 0.7425
year_diff 0.6389
remoteness 0
vegetation_classedOpen Shrubland 0.6595
vegetation_classedPolar Desert/Rock/Ice 0.7391
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.7053
stat_cause_descrCampfire 0.9384
stat_cause_descrChildren 0.003358
stat_cause_descrDebris Burning 0.01335
stat_cause_descrEquipment Use 0.007557
stat_cause_descrFireworks 0.809
stat_cause_descrLightning 0.000000000000000002049
stat_cause_descrMiscellaneous 0.05553
stat_cause_descrMissing/Undefined 0.1047
stat_cause_descrPowerline 0.746
stat_cause_descrRailroad 0.00919
stat_cause_descrSmoking 0.154
stat_cause_descrStructure 0.8422
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
12420 3878 0.1364 0.1349 
lm_se2 <- update(lm_se, . ~ . - stat_cause_descr - PC1 - PC4- year_diff - vegetation_classed)
summary(lm_se2) %>% pander
  Estimate Std. Error t value Pr(>|t|)
(Intercept) -3163 87.46 -36.16 2.37e-272
PC2 -44.3 19.84 -2.233 0.02557
PC3 25.06 18.28 1.371 0.1703
remoteness 19710 458.4 43 0
Fitting linear model: fire_size ~ PC2 + PC3 + remoteness
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
12420 3890 0.1298 0.1296 
lm_mw = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete[which(fire_train_complete$region == "MidWest"),])
summary(lm_mw) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 4277 551.2 7.76
PC1 -380.8 60.1 -6.336
PC2 -124.7 49.19 -2.534
PC3 123 60.17 2.044
PC4 -126.3 74.51 -1.695
year_diff 7.774 13.94 0.5579
remoteness -15485 1866 -8.299
vegetation_classedDesert -274.9 545.5 -0.504
vegetation_classedPolar Desert/Rock/Ice 218.3 183.1 1.192
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 1166 875.2 1.332
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 2718 507.8 5.353
stat_cause_descrCampfire 184.8 507.8 0.3639
stat_cause_descrChildren -217 420.9 -0.5156
stat_cause_descrDebris Burning -326 260.3 -1.252
stat_cause_descrEquipment Use -247.7 341.9 -0.7243
stat_cause_descrFireworks -21.4 692.9 -0.03089
stat_cause_descrLightning 2341 381.2 6.142
stat_cause_descrMiscellaneous -141.6 288.3 -0.4913
stat_cause_descrMissing/Undefined 283.6 411.9 0.6885
stat_cause_descrPowerline 1427 794.8 1.795
stat_cause_descrRailroad -558.4 600.9 -0.9292
stat_cause_descrSmoking -615.1 600.6 -1.024
stat_cause_descrStructure -492.2 1376 -0.3578
  Pr(>|t|)
(Intercept) 0.00000000000001241
PC1 0.0000000002809
PC2 0.01133
PC3 0.04102
PC4 0.09017
year_diff 0.577
remoteness 0.0000000000000001719
vegetation_classedDesert 0.6143
vegetation_classedPolar Desert/Rock/Ice 0.2335
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.1831
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.00000009469
stat_cause_descrCampfire 0.716
stat_cause_descrChildren 0.6062
stat_cause_descrDebris Burning 0.2105
stat_cause_descrEquipment Use 0.4689
stat_cause_descrFireworks 0.9754
stat_cause_descrLightning 0.0000000009517
stat_cause_descrMiscellaneous 0.6232
stat_cause_descrMissing/Undefined 0.4912
stat_cause_descrPowerline 0.07273
stat_cause_descrRailroad 0.3529
stat_cause_descrSmoking 0.3059
stat_cause_descrStructure 0.7205
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
2442 4058 0.09372 0.08548 
lm_mw2 <- update(lm_mw, . ~ . - stat_cause_descr - PC3 - year_diff - PC2)
summary(lm_mw2) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 4417 480.3 9.197
PC1 -494.7 51.56 -9.595
PC4 -85.95 71.69 -1.199
remoteness -13760 1811 -7.599
vegetation_classedDesert -338.4 545.9 -0.6198
vegetation_classedPolar Desert/Rock/Ice 205.3 181.1 1.134
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 841.9 870.7 0.9669
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 3085 506.5 6.092
  Pr(>|t|)
(Intercept) 0.00000000000000000007683
PC1 0.000000000000000000001992
PC4 0.2307
remoteness 0.00000000000004223
vegetation_classedDesert 0.5354
vegetation_classedPolar Desert/Rock/Ice 0.2571
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.3337
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.000000001292
Fitting linear model: fire_size ~ PC1 + PC4 + remoteness + vegetation_classed
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
2442 4105 0.06685 0.06416 
lm_w = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete[which(fire_train_complete$region == "West"),])
summary(lm_w) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 18377 2008 9.151
PC1 -342.2 196.8 -1.739
PC2 502.3 234.5 2.142
PC3 574.3 527.3 1.089
PC4 515 427.7 1.204
year_diff 191.2 54.37 3.516
remoteness -44987 2168 -20.75
vegetation_classedDesert -1175 1601 -0.7339
vegetation_classedOpen Shrubland 2404 2674 0.8988
vegetation_classedPolar Desert/Rock/Ice -222 904.5 -0.2454
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 804.4 1377 0.584
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF -1072 1706 -0.6282
stat_cause_descrCampfire 2517 2612 0.9637
stat_cause_descrChildren -313.2 2934 -0.1068
stat_cause_descrDebris Burning -204.8 2003 -0.1022
stat_cause_descrEquipment Use 1384 1877 0.7376
stat_cause_descrFireworks -3180 4276 -0.7437
stat_cause_descrLightning 2019 1635 1.235
stat_cause_descrMiscellaneous -678.8 1769 -0.3838
stat_cause_descrMissing/Undefined -2706 1971 -1.373
stat_cause_descrPowerline -1045 3399 -0.3075
stat_cause_descrRailroad -1699 3869 -0.4393
stat_cause_descrSmoking -154 3331 -0.04624
stat_cause_descrStructure -3989 8487 -0.47
  Pr(>|t|)
(Intercept) 0.00000000000000000008529
PC1 0.08213
PC2 0.03224
PC3 0.2761
PC4 0.2286
year_diff 0.0004421
remoteness 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000002947
vegetation_classedDesert 0.463
vegetation_classedOpen Shrubland 0.3688
vegetation_classedPolar Desert/Rock/Ice 0.8062
vegetation_classedSecondary Tropical Evergreen Broadleaf Forest 0.5592
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.5299
stat_cause_descrCampfire 0.3353
stat_cause_descrChildren 0.915
stat_cause_descrDebris Burning 0.9186
stat_cause_descrEquipment Use 0.4608
stat_cause_descrFireworks 0.4571
stat_cause_descrLightning 0.2168
stat_cause_descrMiscellaneous 0.7012
stat_cause_descrMissing/Undefined 0.1699
stat_cause_descrPowerline 0.7585
stat_cause_descrRailroad 0.6605
stat_cause_descrSmoking 0.9631
stat_cause_descrStructure 0.6384
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
4352 23598 0.1268 0.1222 
lm_w2 <- update(lm_w, . ~ . - stat_cause_descr - PC3 - PC4 - vegetation_classed)
summary(lm_w2) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) 19539 1151 16.98
PC1 -305.3 162.3 -1.882
PC2 587.4 209.3 2.806
year_diff 187.4 53.68 3.491
remoteness -46518 2044 -22.76
  Pr(>|t|)
(Intercept) 0.00000000000000000000000000000000000000000000000000000000000001116
PC1 0.05992
PC2 0.005032
year_diff 0.0004867
remoteness 1.85e-108
Fitting linear model: fire_size ~ PC1 + PC2 + year_diff + remoteness
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
4352 23602 0.1227 0.1219 
lm_ne = lm(fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr, data = fire_train_complete[which(fire_train_complete$region == "NorthEast"),])
summary(lm_ne) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) -56.05 46.87 -1.196
PC1 -6.488 9.053 -0.7167
PC2 -12.24 6.177 -1.982
PC3 -4.673 6.896 -0.6776
PC4 8.486 8.777 0.9668
year_diff 0.4043 2.001 0.2021
remoteness 1131 68.98 16.39
vegetation_classedDesert -21.49 66.98 -0.3208
vegetation_classedOpen Shrubland -60.52 79.02 -0.766
vegetation_classedPolar Desert/Rock/Ice 28.23 26.09 1.082
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 6.235 35.88 0.1738
stat_cause_descrCampfire -22.07 64.14 -0.3441
stat_cause_descrChildren -26.46 82.96 -0.3189
stat_cause_descrDebris Burning -36.62 39.7 -0.9224
stat_cause_descrEquipment Use -30.52 67.42 -0.4526
stat_cause_descrFireworks 9.788 411.3 0.0238
stat_cause_descrLightning -27.37 62.79 -0.4359
stat_cause_descrMiscellaneous -37.79 33.96 -1.113
stat_cause_descrMissing/Undefined 31.73 65.38 0.4853
stat_cause_descrPowerline -34.26 122.1 -0.2805
stat_cause_descrRailroad -24.84 121.9 -0.2038
stat_cause_descrSmoking -39.33 56.33 -0.6982
stat_cause_descrStructure -31.6 411.3 -0.07682
  Pr(>|t|)
(Intercept) 0.2319
PC1 0.4737
PC2 0.04762
PC3 0.4981
PC4 0.3338
year_diff 0.8399
remoteness 0.00000000000000000000000000000000000000000000000000000004354
vegetation_classedDesert 0.7484
vegetation_classedOpen Shrubland 0.4438
vegetation_classedPolar Desert/Rock/Ice 0.2794
vegetation_classedTemperate Evergreen Needleleaf Forest TmpENF 0.8621
stat_cause_descrCampfire 0.7308
stat_cause_descrChildren 0.7498
stat_cause_descrDebris Burning 0.3564
stat_cause_descrEquipment Use 0.6509
stat_cause_descrFireworks 0.981
stat_cause_descrLightning 0.663
stat_cause_descrMiscellaneous 0.266
stat_cause_descrMissing/Undefined 0.6276
stat_cause_descrPowerline 0.7791
stat_cause_descrRailroad 0.8385
stat_cause_descrSmoking 0.4852
stat_cause_descrStructure 0.9388
Fitting linear model: fire_size ~ PC1 + PC2 + PC3 + PC4 + year_diff + remoteness + vegetation_classed + stat_cause_descr
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
1689 409.1 0.1588 0.1477 
lm_ne2 <- update(lm_ne, . ~ . - stat_cause_descr - vegetation_classed - year_diff - PC4 - PC3 - PC2)
summary(lm_ne2) %>% pander
Table continues below
  Estimate Std. Error t value
(Intercept) -44.59 13.83 -3.225
PC1 -10.2 7.279 -1.401
remoteness 1103 64.76 17.03
  Pr(>|t|)
(Intercept) 0.001286
PC1 0.1614
remoteness 0.000000000000000000000000000000000000000000000000000000000004196
Fitting linear model: fire_size ~ PC1 + remoteness
Observations Residual Std. Error \(R^2\) Adjusted \(R^2\)
1689 407.9 0.1539 0.1529

The whole region’s RMSE is 10,325.41. We use it for comparing the model’s performance. The model performance will be checked with RMSE.

whole_pred = predict(lm_whole2, newdata = fire_test_complete)

test_MSE <- mean((fire_test_complete$fire_size - whole_pred)^2)

#print test RMSE
whole_test_RMSE = sqrt(test_MSE)
sw_pred = predict(lm_sw2, newdata = fire_test_complete[which(fire_test_complete$region == "SouthWest"),])

sw_test_MSE <- mean((fire_test_complete$fire_size[which(fire_test_complete$region == "SouthWest")] - sw_pred)^2)

#print test RMSE
sw_test_RMSE = sqrt(sw_test_MSE)

se_pred = predict(lm_se2, newdata = fire_test_complete[which(fire_test_complete$region == "SouthEast"),])

se_test_MSE <- mean((fire_test_complete$fire_size[which(fire_test_complete$region == "SouthEast")] - se_pred)^2)

#print test RMSE
se_test_RMSE = sqrt(se_test_MSE)

mw_pred = predict(lm_mw2, newdata = fire_test_complete[which(fire_test_complete$region == "MidWest"),])

mw_test_MSE <- mean((fire_test_complete$fire_size[which(fire_test_complete$region == "MidWest")] - mw_pred)^2)

#print test RMSE
mw_test_RMSE = sqrt(mw_test_MSE)

w_pred = predict(lm_w2, newdata = fire_test_complete[which(fire_test_complete$region == "West"),])

w_test_MSE <- mean((fire_test_complete$fire_size[which(fire_test_complete$region == "West")] - w_pred)^2)

#print test RMSE
w_test_RMSE = sqrt(w_test_MSE)

ne_pred = predict(lm_w2, newdata = fire_test_complete[which(fire_test_complete$region == "NorthEast"),])

ne_test_MSE <- mean((fire_test_complete$fire_size[which(fire_test_complete$region == "NorthEast")] - ne_pred)^2)

#print test RMSE
ne_test_RMSE = sqrt(ne_test_MSE)

table_lm = data.frame(Region = c("Whole US", "North East", "Mid West", "West", "South West", "South East"),
                      RMSE = c(whole_test_RMSE, ne_test_RMSE, mw_test_RMSE, w_test_RMSE, sw_test_RMSE, se_test_RMSE),
                      NumberofObservation = c(length(whole_pred),length(ne_pred),length(mw_pred),length(w_pred),length(sw_pred),length(se_pred)))
kable(table_lm, caption = "Linear Model's RMSE")
Linear Model’s RMSE
Region RMSE NumberofObservation
Whole US 10228.90 6713
North East 20688.09 435
Mid West 5640.77 630
West 15576.66 1058
South West 11565.08 1581
South East 3281.71 3009

2.4.1 K Nearest Neighbor

KNN (short for K Nearest Neighbor) is a non-linear algorithm that works for both classification and regression problems. The basic premise behind the model is that it predicts the dependent variable based on how similar they are to other observations where the dependent variable is known.

KNN works by calculating euclidean distance between observations, so all inputs have to be numeric. Therefore, we have to do some pre-model data changes to our training and test sets. For both test data and training data we dummy code categorical variables, then we center and scale the data. As before, we assume that the training and test data are completely separated, so we process the two data sets separately.

#first we dummy code categorical variables (what about ordinal?)
knn_ready_train <- dummy_cols(fire_train_complete, select_columns = 
                                c("stat_cause_descr", "region", "vegetation_classed", "season")) %>% 
  #then we get rid of non-dummy coded variables
  select(-stat_cause_descr, - region, - vegetation_classed, -season) %>% 
  #then convert back to a data frame (as output for `dummy_cols` is a matrix)
  as.data.frame()

#then we center and scale the data, except our outcome
knn_ready_train[,-1] <- scale(knn_ready_train[,-1], center = T, scale = T)


#of course our next step is to do the same to the test data
knn_ready_test <- dummy_cols(fire_test_complete, 
                             select_columns = c("stat_cause_descr", "region", "vegetation_classed", "season")) %>% 
  select(-stat_cause_descr, - region, - vegetation_classed, -season) %>% 
  as.data.frame()

knn_ready_test[,-1] <- scale(knn_ready_test[,-1], center = T, scale = T)

Next we split up the training and test data into a data frame that has only independent variables and a data frame that has only dependent variables (in this case fire_size). We do this for both the test and the training data.

#YTrain is the true values for fire size on the training set 
YTrain = knn_ready_train$fire_size

#XTrain is the design matrix for training data
XTrain =  knn_ready_train %>% 
  select(-fire_size)
 
#YTest is the true value for fire_size on the test set
YTest = knn_ready_test$fire_size

#Xtest is the design matrix for test data
XTest = knn_ready_test %>% 
  select(-fire_size)

Then we use Leave One Out Cross Validation to determine the best number of neighbors to consider. A low number of neighbors considered results in a highly flexible model, while a higher number results in a less flexible model. For this process we built a function which we enter a starting value of K, an ending value of K, and the sampling interval. The result is a data frame of MSE values for each value of K that we test. This process is computationally intensive so we automatically saved results to a csv.

#make a function that saves KNN LOOCV results for different values of K
knn_loocv <- function(startk, endk, interval)
  {
  
#set up possible number of nearest neighbors to be considered 
allK = seq(from = startk, to = endk, by = interval)

#create a vector of the same length to save the MSE in later
k_mse = rep(NA, length(allK))

#for each number in allK, use LOOCV to find a validation error  
for (i in allK){  
  #loop through different number of neighbors
  #predict on the left-out validation set
  pred.Yval = knn.cv(train = XTrain, cl = YTrain, k = i) 
  #find the mse for each value of k
  k_mse[i] = mean((as.numeric(pred.Yval) - YTrain)^2)
}

#save as a data frame and filter out NAs (caused by skipping values of k if interval is larger than 1)
k_mse <- as.data.frame(k_mse) %>% 
  filter(!is.na(k_mse))

#bind with k value
knn_loocv_results <- cbind(as.data.frame(allK), k_mse)

#save MSE as CSV (because the cross validation process takes a long time)
write_csv(knn_loocv_results, paste0("model_results/knn/knn_mse_k", startk,"_k", endk, "_by", interval, ".csv"))

}

#we tried several different sets of k
knn_loocv(startk = 1, endk = 20, interval = 1)
knn_loocv(startk = 1, endk = 500, interval = 20)

Next, we go through our results for all the values of K that we tested. We find that the MSE increases as K increases.

#read in all the stored k values
knn_mse_k1_k500_by20 <- read_csv(here("model_results", "knn", "knn_mse_k1_k500_by20.csv"))

knn_mse_k1_k20_by1 <- read_csv(here("model_results", "knn", "knn_mse_k1_k20_by1.csv"))

#plot MSE for values of k
plot(knn_mse_k1_k500_by20$allK, knn_mse_k1_k500_by20$k_mse, type = "l", xlab = "k", ylab = "MSE", main = "MSE for K 1 through 500 at intervals of 20")

When we look at K 1-20 we get the lowest MSE at around 3 before it starts increasing.

plot(knn_mse_k1_k20_by1$allK, knn_mse_k1_k20_by1$k_mse, type = "l", xlab = "k", ylab = "MSE", main = "MSE for K 1 through 20 at intervals of 1")

Just to confirm, we will print out the best number of neighbors.

#best number of neighbors
numneighbor = max(knn_mse_k1_k20_by1$allK[knn_mse_k1_k20_by1$k_mse == min(knn_mse_k1_k20_by1$k_mse)])

#print best number of neighbors
numneighbor
## [1] 2

Now that we’ve found the best number of nearest neighbors to consider, we try out KNN on our test data! Below is the test MSE and the test RMSE.

#fit KNN model with best neighbor value to test data
pred.YTest = knn(train = XTrain, test = XTest, cl = YTrain, k = numneighbor)

#predict KNN
test_MSE <- mean((as.numeric(pred.YTest) - YTest)^2)

#print test MSE
test_MSE
## [1] 83373364
#print test RMSE
sqrt(test_MSE)
## [1] 9130.902

Over all, this model performs okay.

2.4.2 Boosted Tree

#train boosted tree model
fire_size_boost = gbm(fire_size~., 
                      data = fire_train,
                      n.trees = 500, 
                      interaction.depth = 4
                    )

#the model summary creates a pretty visualization
summary(fire_size_boost)

#calculate training error

#predict values using training data
predictions_train_boost <- predict(fire_size_boost, data = fire_train)

#calculate rmse for training data
RMSE(predictions_train_boost, fire_train$fire_size)

#calculate test error

#predict values using test data
predictions_test_boost <- predict(fire_size_boost, data = fire_test)

#calculate rmse for training data
RMSE(predictions_test_boost, fire_test$fire_size)

2.4.3 Random Forest

#train model
fire_size_rf = randomForest(fire_size ~ ., #writing the formula
                          data = fire_train_complete, #specifying training data to be used
                          mtry = 9, #setting number of variables to randomly sample per each split
                          ntree= 500, #setting number of trees
                          mode = "regression", #specifying regression
                          na.action = na.omit, #specifying what to do with NAs
                          importance = TRUE #specifying importance of variables should be assessed
                          )
#plot error
plot(fire_size_rf)

#plot variable importance
varImpPlot(fire_size_rf, 
           sort = T, 
           main = "Variable Importance for fire size random forest model", 
           n.var = 5)

#calculate training error

#predict values using training data
predictions_train_rf <- predict(fire_size_rf, data = fire_train)

#calculate rmse for training data
RMSE(predictions_train_rf, fire_train$fire_size)

#calculate test error

#predict values using test data
predictions_test_rf <- predict(fire_size_rf, data = fire_test)

#calculate rmse for training data
RMSE(predictions_test_rf, fire_test$fire_size)

what type of modeling will we do? we must try 4 types

  • neural network

3 Results

predictions without climate change

How do predictions change with 2.5C increase in temp?

4 Conclusion